1. Working in different contexts: RStudio Projects
2. Dynamic document generation: RMarkdown
3. Version control: Git + GitHub
4. Package management: renv
5. Containerization: Docker
6. Where to start?

• Peikert, A., & Brandmaier, A. M. (2020). A Reproducible Data Analysis Workflow with R Markdown, Git, Make, and Docker. PsyArXiv Preprints. https://doi.org/10.31234/osf.io/8xzqy

• Andreas Brandmaier: “A Reproducible Data Analysis Workflow with R Markdown, Git, Make, and Docker”, talk at the Online Symposium on Reproducing Analyses in Biological Psychology, November 2020 (https://www.youtube.com/watch?v=nTVcMDVlyOI)
• Richard McElreath: “Science as Amateur Software Development”, talk at the Max Planck IT Community, August 2020 (https://www.youtube.com/watch?v=zwRdO9_GGhY)
• Russ Poldrack: “Toward a Culture of Computational Reproducibility”, talk at the Foundations of Biomedical Data Science, December 2020 (https://www.youtube.com/watch?v=XjW3t-qXAiE)

• What it does:
  • Allows to work in multiple different contexts (projects), e.g. one for each experiment
  • Each project is own working directory, workspace, history, and source documents
  • Each project is associated with a folder on your computer (= working directory)
• Why it helps:
  • Have a separate, shareable working environment for each experiment
  • Keep all the files associated with a project together — data, scripts, results, figures
  • Work on multiple projects at once, each associated with its packages (and package versions), loaded data, etc.
  • Use only relative paths
  • Necessary basis for version control

• In RStudio: File > New Project > …

• Relative paths: path separator characters vary across systems & anchor points differ depending on contexts
  • Use the here-package (Müller, 2020) to define relative paths within the project: read.csv(here::here("data", "file_I_want.csv"))

• What it does:
  • Creates dynamic documents with embedded chunks of code (R, Python, Julia, Stan, …), computed results , written text etc. (= LaTeX)
  • Markdown-files can be exported to documents (docx, rtf), presentations, pdfs, websites (html), … e.g using the knitr (Xie, 2015, 2020) and tinytex (Xie, 2015, 2020; for pdfs)
  • R code is dynamically rendered, and can be given in separate chunks (’’‘{r}’’‘) or inline (’ r … ’)
• Why it helps:
  • Simple language (\(\neq\) LaTeX)
  • Integrates directly with statistical software (RStudio)
  • Saves code AND output in one file
  • Reduces copy & paste errors: reported results consistent with actual results

• Installation: install.packages("rmarkdown") (Allaire et al., 2017)
• Install ‘knitr’ package for easy access: install.packages("knitr") (Xie 2015, 2020)

• Installation: install.packages("rmarkdown") (Allaire et al., 2017)
• Install ‘knitr’ package for easy access: install.packages("knitr") (Xie 2015, 2020)
• Open a markdown file (.Rmd): File > New File > R Markdown

• Installation: install.packages("rmarkdown")
• Open a markdown file: File > New File > R Markdown

• You don’t have RStudio installed: install Pandoc (http://pandoc.org) before installing markdown ()
• Lengthy R code chunks: Install knitr-package (Xie, 2014, 2015, 2020) to customize chunks and knitting process
  • {r cache=TRUE,message=FALSE,warning=FALSE,results="hide", error = TRUE}
  • or use opts_chunk$set()-function
• Knit to pdf: You need a LaTeX-installation
  • TinyTeX (Xie, 2010) is a light-weight, cross-platform distribution (install.packages("tinytex"); tinytex::install_tinytex()))
  • Separate code chunks by a blank line
• Knit older .R code files: Put #’ in front of any top-level prose, including the header, or use:

#/*
rmarkdown::render(input = rstudioapi::getSourceEditorContext()$path,
                  output_format = rmarkdown::github_document()),
                  knit_root_dir = getwd()) #*/

• What it does:
  • Tracks changes to files (data and code) over time: Sequence of “snapshots” (commits)
  • Allows to “go back in time”: Recall older versions or revert the entire project
  • Changes between commits can be compared
  • Organized in repositories: Collection of all snapshots
  • GitHub: Popular server for sharing materials (privately or publicly) and collaborating via git (also: GitLab and others)

• Why it helps:
  • Keep things organized and track changes
  • Clean up code
  • Language agnostic
  • (Remote) backup
  • Work together, with collaborators (even simultaneously and parallel: branches, merges, pull requests) - and your future self
  • Web interface for your project and to track issues
  • Easily connected e.g. to osf.io

• Register an account with GitHub: https://github.com/
• (Update R, RStudio, and your packages: update.packages(ask = FALSE, checkBuilt = TRUE))
• Is Git installed? Open your shell (“Terminal” in RStudio or on Mac, “Eingabeaufforderung” on Windows), and type: git --version. If “git: command not found”:
• Install Git - Mac: Mac offers to install developer command line developer tools automatically. Click “Install”. If you don’t get the offer, type: xcode-select --install. Restart R.
• Install Git - Windows: Install “Git Bash” (https://gitforwindows.org). Accept default settings. When asked about “Adjusting your PATH environment”, select “Git from the command line and also from 3-rd party software”. Restart R.
• Configure Git: In the (Git Bash) shell, type
  • git config --global user.name 'your name'
  • git config --global user.email 'email associated with your GitHub account'
  • git config --global --list (Check whether everything worked)
• Optional: Install a Git client. Find more info e.g. here: https://happygitwithr.com/git-client.html

• Vocabulary - Git:
  • Repo(sitory): Directory of files that Git manages holistically
  • Commit: Snapshot of all files in the repository, at a specific moment, each with a unique identifier (hash code or SHA) and description (commit message)
  • Diff: Set of differences between (any) two commits
  • Tag: Specific name for a certain snapshot (optional), e.g. “v1.0.3”, “preprint”, “submitted”

• Vocabulary - Git:
  • Repo(sitory): Directory of files that Git manages holistically
  • Commit: Snapshot of all files in the repository, at a specific moment, each with a unique identifier (hash code or SHA) and description (commit message)
  • Diff: Set of differences between (any) two commits
  • Tag: Specific name for a certain snapshot (optional), e.g. “v1.0.3”, “preprint”, “submitted”
• Vocabulary - GitHub
  • Push: Send your local Git commits to GitHub
  • Pull: Compare and update your local Git with GitHub
  • Merge conflict: Git can’t be certain how to jointly apply diffs from two commits to their common parent. Resolve by picking manually, avoid by pushing often.

• Go to https://github.com/ and log in
• Click “New repository”
  • Decide between “private” or “public”. Initialize with a README. Accept default for everything else.
  • Click “Create repository”
  • Copy the HTTPS

• Clone your GitHub repo to your computer: Type git clone https://github.com/YOUR-USERNAME/YOUR-REPOSITORY.git (your link) in the shell (Terminal in RStudio or on Mac, Git Bash on Windows)
  • Make this repo your working directory (cd YOUR-REPOSITORY), list its files (ls), display README (head README.md), get info on its connection to GitHub (git remote show origin)
  • Make a local change: Add a new line to README, and verify change is noticed:

echo "This is the first change to my repo" >> README.md
git status

• Stage (add), commit (commit - m "YOUR-COMMIT-MESSAGE"), and push change. You may be asked for your username and password.

git add -A
git commit -m "A commit from my local computer"
git push

- (Clean up: Delete your local repo (`cd`, and then `rm -rf YOUR-REPO-NAME/`))

• Clone your repository to RStudio
  • File > New Project > Select “Version Control” > Select “Git” > Enter your repository URL: https://github.com/YOUR-USERNAME/YOUR-REPOSITORY.git

• GitHub: No long-term guarantee for availability of service (is commercial)
  • Mirror snapshots on HU servers/OSF/Zenodo/FigShare/…
• GitHub: .md-files will be displayed like HTML, CSV will have a nice layout, README.md-files act like the landing page. Use internal link to other files.

• What it does:
  • Creates a project-specific library of packages in the project folder
  • Overwrites install.packages() to install packages in this local library
  • Keeps track of package versions in the renv.lock file

• Why it helps:
  • Keeps package versions untouched by other projects
  • Allows you to revert to the previous state when an update has broken your analysis
  • Makes it easier to share package versions with your collaborators (e.g., via GitHub)
  • Can also keep track of Python packages

1. Install renv just like any other R package via install.packages(renv)
2. Initialize your project library via renv::init()
   (Instead, you can also select “Use renv with this project” during project creation)
3. After successfully installing or updating packages, use renv::snapshot()
4. If you want to revert to previous state (e.g., if an update caused problems), use renv::restore()

• Initialize renv for your sleepstudy project using renv::init()
• From the “Files” pane in RStudio, take a look at the renv.lock file
• Install a new package:

install.packages("cowsay")

• Actually use the package in one of your scripts (or .Rmd files):

cowsay::say("Hello world", "cow")

• Write this change to the lockfile using renv::snapshot()
• Commit and push your changes to GitHub

Restoring someone else’s package versions:

1. Clone or pull the repository from GitHub
2. Open the the RStudio project (e.g. via the projectname.Rproj file)
3. Use renv::restore() to install the package versions from the renv.lock file

• There may be some (inconsequential) warnings when switching between Mac and Windows
• At least on Windows, you need to have Rtools installed when installing packages that are not on CRAN (https://cran.r-project.org/bin/windows/Rtools/)
• Installing and loading packages may take a while, especially if your project lives on a network drive
  (such as N:/)

• What it does:
  • Creates a small, linux-based virtual machine on your computer
  • Makes it possible to run your scripts (or render your .Rmd files) on this virtual system
  • The recipe to build this system is stored in a Dockerfile that can be shared via GitHub

• Why it helps:
  • Prevents differences between operating systems, R versions, region and language settings etc.
  • Ensures long-term reproducibility
  • Provides a starting point for cloud-based and high perfomance computing (HPC)
  • Pre-packaged Docker images are available for different languages (R, Python, MATLAB, LaTeX etc.)

• Install Docker from https://docs.docker.com/installation/
• From the terminal, start a R/RStudio container and mount your local project folder:

docker run -d  -e PASSWORD=1234 -p 8787:8787 -v /path/to/your/project:/home/rstudio/ rocker/rstudio

• You can then access RStudio (running in the container) by opening http://localhost:8787 in your web browser (username: rstudio, password: 1234)
• You can also build your own container by:
  • Choosing a base image from https://hub.docker.com/u/rocker (including the tidyverse, LaTeX etc.)
  • Creating a Dockerfile in your project directy, specyfing additional steps to execute when building the container, e.g., install.packages("renv"); renv::restore()

• For detailled instructions, see Boettiger & Eddeulbuettel (2017) and
  Peikert & Brandmaier (2020)

• Example for a Dockerfile:

# This as a text file stored with the name "Dockerfile" in your project directory.

# Base image from Docker Hub, including R, RStudio, the tidyverse, and LaTeX
FROM rocker/verse:4.0.2

# Set working directory within the container
WORDIR /home/rstudio

# Install renv
RUN R -e "remotes::install_version('renv', version = '0.12.0', repos = 'http://cran.us.r-project.org')"

# Copy the lock file
COPY renv.lock renv.lock

# Install package versions stored in the lockfile
RUN R -e "renv::consent(provided = TRUE)"
RUN R -e "renv::restore(prompt = FALSE)"

• Some additional tools based on Docker:
  • With binder (https://mybinder.org) and Code Ocean (https://codeocean.com), you can run your analysis in the cloud; they will even create the Dockerfile for you if you don’t have your own one
  • Singularity (https://sylabs.io) is a fully compatible, open source clone of Docker which you can use on systems where you don’t have root access (e.g., on high performance clusters)

• This wealth of tools can seem overwhelming
  • Adopting even one or two of them can help making your code more reproducbile
• An RStudio project and renv are easy to set up even for existing projects
  • And will help a lot to make sure that you can still run your code at re-submission
• Version control is best tried out with a new (real or toybox) project
  • Create an empty repository on GitHub and use it to create your RStudio project
• Once you’ve made it this far, full computational reproduciblity (by containerizing your project) is just one more step away

• Create a GitHub repository: Go to https://github.com/ > Enter your username and password > Click “New” Repository > Settings: Create a private repository (you can make it public later), add a README file, accept default settings for everything else. Click “Create repository” > Copy the URL
• Open R Studio
• Create an R project: File > New Project… > Select Version Control > Select Git > Enter the repository URL (the URL you just copied: <https://github.com/USERNAME/REPOSITORY-NAME), choose a project directory name and where it should be saved. Click “Create Project”.
• Install RMarkdown: Type to console install.packages("rmarkdown") and install.packages("knitr")
• Create an R Markdown file: File > New File > R Markdown… > Select “Document” > Choose a title (e.g. “analyses_sleepstudy”) and HTML as default output format. Click “OK”.
• Make changes to your Markdown file: Enter a first section title (`#Random number generation), a text (“Here, we generate 10 random numbers between 0 and 10”), and an r code chunk ({r sample(0:10, 10, replace = FALSE} )